Pre-season favourites for the wooden spoon, the Phoenix can be satisfied with their efforts but that will prove scant consolation as they begin their long journey home.
Predictions of a tense, guarded affair failed to materialise in the opening 10 minutes, with the two sides attacking each other at will. Perth were first to work the goalkeeper when Mark Paston was required to turn around the post a flicked header from Travis Dodd, and from the resulting corner the Glory went ahead.
Vince Lia's blushes were spared when his goal-bound header was cleared was off the line by Tony Lochhead, but the ball fell to Bas van den Brink and the Dutch defender smashed an unstoppable shot into the roof of the net for his first ever Glory goal.
Despite falling behind, the Phoenix had the better of the first half. They edged the all-important battle in midfield and played some pretty football, though that counted for little as Danny Vukovic went untested in the Perth goal.
That changed almost immediately after the halftime break, as Greenacre emphatically drew the Phoenix level with his fifth goal of the season. A fine counter-attacking move saw Tim Brown chest down Leo Bertos' cross for Greenacre to lace in a volley from the edge of the area.
And it soon got better for Wellington. Lia picked out Muscat's run from defence and the right back cut in and curled a delightful left-footed shot around Vukovic and into the bottom corner.
It was a remarkably quick turnaround for the Phoenix but the lead was no more than they deserved. Their chances of holding that lead, however, took a blow with half an hour to play when Ben Sigmund was forced from the field.
Sigmund's absence was soon felt as the Glory found an equaliser. Muscat, who moved into the middle in place of the All White, gave Billy Mehmet too much room and the striker slotted Shane Smeltz's fortuitous flick under Paston to lock up the game.
The final 20 minutes were, unsurprisingly, cagey before Smeltz had a chance to send home his former side in stoppage time. Thankfully for the Phoenix, the A-League's all-time leading scorer shot tamely straight at Paston, and to extra time the game went.
The home side had the better of the first period of extra time, as a jaded-looking Phoenix spent much of the 15 minutes camped in their half, but the Glory never seriously threatened to find the vital goal.
That was until Howarth got on the end of a clever Scott Neville pass to send the Phoenix packing and end the retiring Brown's football career.
PERTH GLORY 3 (Bas van den Brink 13m, Billy Mehmet 72m, Todd Howarth 112m) bt WELLINGTON PHOENIX 2 (Chris Greenacre 47m, Manny Muscat 55m) after extra time at nib Stadium. Crowd: 13,695. Referee: Peter Green.
